I keep getting this message when running cuffdiff "This job was terminated because it used more memory than it was allocated", I've read the wiki thread and the only way I can bypass this is if I set up my own instance of galaxy on the cloud.

This specific tool already executes with maximum memory allocation on the cluster at http:/usegalaxy.org.

Choosing options that reduce memory utilization are sometimes possible. The same memory-intensive options used line-command also apply when executed within Galaxy. The manual explains these in more comprehensive detail: http://cole-trapnell-lab.github.io/cufflinks/

However, those changes may not meet your analysis needs or the data may be too large to processes even with the changes. A local or cloud is the only solution for these cases (it is doubtful that other public Galaxy servers allocate more memory - but you could try for those that offer open accounts).
https://wiki.galaxyproject.org/BigPicture/Choices